#' Wrapper to run fisher's test on presence/absence of a feature.
#' 
#' This function returns a data frame of p-values, odds ratios, lower and upper
#' confidence limits for every row of a matrix.
#' 
#' 
#' @param obj A MRexperiment object with a count matrix, or a simple count
#' matrix.
#' @param cl Group comparison
#' @param thres Threshold for defining presence/absence.
#' @param adjust.method Method to adjust p-values by. Default is "FDR". Options
#' include "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr",
#' "none". See \code{\link{p.adjust}} for more details.
#' @param cores Number of cores to use.
#' @param ... Extra parameters for makeCluster
#' @return Matrix of odds ratios, p-values, lower and upper confidence intervals
#' @seealso \code{\link{cumNorm}} \code{\link{fitZig}} \code{\link{fitDO}} \code{\link{fitMeta}}
#' @examples
#' 
#' data(lungData)
#' k = grep("Extraction.Control",pData(lungData)$SampleType)
#' lungTrim = lungData[,-k]
#' lungTrim = lungTrim[-which(rowSums(MRcounts(lungTrim)>0)<20),]
#' res = fitPA(lungTrim,pData(lungTrim)$SmokingStatus);
#' head(res)
#'
fitPA<-function(obj,cl,thres=0,adjust.method='fdr',cores=1,...){
    x = returnAppropriateObj(obj,norm=FALSE,log=FALSE)>thres
    nrows= nrow(x);
    if(is.null(rownames(x))){rownames(x)=1:nrows}

    nClass1 = sum(cl==levels(cl)[1])
    nClass2 = sum(cl==levels(cl)[2])

    cores <- makeCluster(getOption("cl.cores", cores),...)
    res = parRapply(cl=cores,x,function(i){
            tbl = table(1-i,cl)
            if(sum(dim(tbl))!=4){
                tbl = array(0,dim=c(2,2));
                tbl[1,1] = sum(i[cl==levels(cl)[1]])
                tbl[1,2] = sum(i[cl==levels(cl)[2]])
                tbl[2,1] = nClass1-tbl[1,1]
                tbl[2,2] = nClass2-tbl[1,2]
            }
            ft <- fisher.test(tbl,workspace=8e6,alternative="two.sided",conf.int=TRUE)
            cbind(o=ft$estimate,cl=ft$conf.int[1],cu=ft$conf.int[2],p=ft$p.value)
        })
    stopCluster(cores)
    nres = nrows*4
    seqs = seq(1,nres,by=4)
    p = res[seqs+3]
    adjp = p.adjust(p,method=adjust.method)
    o = res[seqs]
    cl = res[seqs+1]
    cu = res[seqs+2]
    res = data.frame(cbind(o,cl,cu,p,adjp))

    colnames(res) = c("oddsRatio","lower","upper","pvalues","adjPvalues")
    rownames(res) = rownames(x)
    return(res)
}